Reporting GO slim results, why shouldn't I display my "GO slim" results as a pie chart ?

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The numbers provided by a GO slim are an annotation count not a gene product count, and so gene products may be present in more than one bin. Therefore displaying GO slim totals as percentages is not meaningful. For your results to be interpreted fully, you should also report how many genes are annotated but not in your slim, and how many genes do not slim.